Global authentication files are useful if you connect to a variety of hosts, where you can log in with the same public/private (identity) key file.
These files are used for a login, when you make a connection via Quick Connection or via Host Directory and if you choose 'Global SSH Key Files' there for the ssh key field. Otherwise, usage depends on the option to always use the global key files for all connections.
The Global Authentication Files dialog lets you specify three different types of public/private key files.
See also: SSH Communication→Options
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